CELLxGENE logoCollectionsDatasetsGene ExpressionCell Guide

  • CellxGene
  • Find Published Data
  • Contribute and Publish Data
  • Download Published Data
  • Analyze Public Data
    • Get Started
    • Hosted Tutorials
    • Gene Expression Documentation
      • Get Started
      • Cell Type and Gene Ordering
      • Gene Expression Data Processing
      • Available Tissues
      • Find Marker Genes
      • Gene Expression Source Data
  • Annotate and Analyze Your Data
    • Get Started
    • Getting Started: Install, Launch, Quick Start
    • Self Host cellxgene
    • Preparing Data
    • Annotating Data
    • Automatic Annotation
    • Gene Sets
    • Community Extensions
    • Multimodal Annotations
  • Join the CellxGene User Community
  • Cite cellxgene in your publications
  • Frequently Asked Questions
  • Learn About Single Cell Data Analysis

Welcome to CZ CELLxGENE

CELLxGENE is a suite of tools that help scientists to find, download, explore, analyze, annotate, and publish single cell datasets. It includes several powerful tools with various features to help you to engage with single cell data.

Clicking on the links below will take you to the tutorials for the relevant task.


Find and download any of the data sets published on CELLxGENE.

Main Tasks: Find Public Data, Download Public Datasets


Once you find a published dataset of interest on CELLxGENE Discover, you can click on the explore button below the dataset description to explore the cells of that dataset using the CELLxGENE Explorer.

Main Tasks: Explore & Analyze Individual Public Datasets

Gene Expression

Gene Expression allows for exploration of gene expression by cell type across all data sets in the CELLxGENE Discover data corpus. It is currently in beta.

Main Tasks: Explore & Analyze Multiple Data Sets in the Public Data Corpus


A PyPI package to explore and annotate single cell datasets you upload into the tool and explore unpublished single cell data.

Main Tasks: Analyze & Annotate Private Data, Share & Analyze Private Datasets

Interested in publishing your data on CELLxGENE Discover? Learn more here

Contact Us

Questions? Contact us at: cellxgene@chanzuckerberg.com